Illumina Paired-end Data Research Articles

The complete sequence of chloroplast genome of Baeckea frutescens Linaeus 1753 (Myrtoideae), a traditional folk medicinal plant

Baeckea frutescens Linaeus 1753, as a traditional folk medicine in South East Asia, possesses sesquiterpenes, phloroglucinols, chromones, and essential oil, and is utilized for traditional Chinese medicinal purposes. The genetic diversity of the plant must be better understood, considering its significance. The complete chloroplast (cp) genome of B. frutescens was sequenced and assembled by using Illumina paired-end data, marking a significant advancement toward comprehending its genetic composition. The complete cp genome is 158,939 bp in length and contains 128 genes, consisting of 83 protein-coding genes, 8 ribosomal RNA genes, and 37 transfer RNA genes. Phylogenetic analyses indicated that B. frutescens and other the 13 were clustered to the family of Myrtaceae. These findings are crucial for the conservation and utilization of this important plant species. Additionally, they underscore the potential for future research on the evolution and preservation of B. frutescens, which could be advantageous in pharmaceutical applications.

The complete chloroplast genome of Prunus phaeosticta (Hance) Maxim. (Rosaceae) and its phylogenetic implications

The complete chloroplast (cp) genome of Prunus phaeosticta (Hance) Maxim. has been characterized by reference-based assembly using Illumina paired-end data. The circular complete cp genome is 158,752 bp in length, comprising a large single-copy (LSC) region of 87,085 bp, a small single-copy (SSC) region of 18,923 bp, and a pair of inverted repeats (IRs) of 26,372 bp.A total of 129 functional genes were identified, including 84 protein-coding genes, 37 tRNA genes, and 8 ribosomal RNA genes. The phylogenetic analysis showed that P. phaeosticta displayed a kinship to Prunus zippeliana.

The complete chloroplast genome of Rubus pacificus (Rosaceae)

The complete chloroplast genome of Rubus pacificus, a representative species of R. sect. Malachobatus subsect. Stipulosi, has been characterized by reference-based assembly using Illumina paired-end data. The complete chloroplast genome is 156,255 bp in length, containing a large single-copy region (LSC) of 85,864 bp and a small single-copy region (SSC) of 18,849 bp, which are separated by a pair of inverted repeat regions (IR) of 25,771 bp. A total of 129 genes were predicted from the chloroplast genome, including 85 protein-coding genes, 36 tRNA genes, and eight rRNA genes. According to the present sampling, phylogenetic analysis reveals that R. pacificus and R. laciniatostipulatus form a strongly supported clade and R. sect. Malachobatus subsect. Stipulosi is not monophyletic.

The complete chloroplast genome sequence of Quercus sessilifolia Blume (Fagaceae)

Quercus sessilifolia Blume is one of the dominant tree species in East Asian evergreen broadleaved forests. In this study, we assembled and characterized the plastome of Q. sessilifolia using Illumina paired-end data. The circular genome is 160,813 bp in size, consisting of two copies of inverted repeat (IR) regions of 25,862 bp, one large single-copy (LSC) region of 90,218 bp, and one small single-copy (SSC) region of 18,871 bp. It encodes a total of 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 28 chloroplast genome sequences indicated that Q. sessilifolia was most closely related to Q. myrsinifolia with 90% bootstrap support.

The complete chloroplast genome of Narcissus ‘Pink Charm’

The first complete chloroplast (cp) genome of Narcissus ‘Pink Charm’ was sequenced and characterized using Illumina paired-end data. The assembled cp genome was 159,988 in length with a GC content of 37.82%. A total of 137 genes were annotated, consisting of 91 protein-coding genes, eight ribosomal RNA genes, and 38 transfer RNA genes. The phylogenetic position based on the cp genome data revealed that Narcissus ‘Pink Charm’ is more closely related to Narcissus poeticus than other relative species.

Characterization of the complete chloroplast genome of Lonicera similis (Caprifoliaceae)

The complete chloroplast genome of Lonicera similis Hemsl. has been characterized by reference-based assembly using Illumina paired-end data. The circular complete cp genome is 155,463 bp in length, containing a large single copy (LSC) region of 89,282 bp, a small single copy (SSC) region of 18,661 bp, which are separated by a pair of inverted repeat (IR) regions of 23,760 bp. A total of 129 genes were predicted from the cp genome, including 83 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Phylogenetic analysis reveals that L. similis is more closely related to Lonicera japonica Thunb. and Lonicera dasystyla Rehd. Our result will provide a reference for the phylogenetic relationship, plant identification and resource development and utilization of Lonicera species.

Complete chloroplast genome sequence of Convolvulus arvensis

The complete chloroplast genome of Convolvulus arvensis was reconstructed by reference-based assembly using Illumina paired-end data. The assembled plastome is 153,234 base pairs (bp) in length, including a pair of inverted repeat regions (IRs) of 22,662 bp each, a large single-copy region (LSC) of 89,059 bp and a small single-copy region (SSC) of 19,651 bp. A total of 115 genes were predicted from the chloroplast genome, including 74 protein coding genes, 37 tRNA genes and 4 rRNA genes. The overall GC content of C. arvensis chloroplast genome was 37.7%. Phylogenetic analysis with several reported chloroplast genomes showed that C. arvensis is closely clustered with Operculina macrocarpa. The complete chloroplast genome of C. arvensis provides new insight into the evolutionary and genomic studies of Convolvulaceae.

Chromosome-Scale Genome Assembly of Talaromyces rugulosus W13939, a Mycoparasitic Fungus and Promising Biocontrol Agent.

Here, we report a chromosome-level genome assembly of Talaromyces rugulosus (syn. Penicillium rugulosum) W13939 (six chromosomes; contig N50: 5.90 Mb), generated using a combination of PacBio long-read and Illumina paired-end data. T. rugulosus is not only a potent enzyme producer, but also a mycoparasite of Aspergillus flavus, which is a notorious plant pathogen and mycotoxin producer, making it a promising biocontrol agent. The T. rugulosus genome is rich in genes encoding proteases, carbohydrate-active enzymes, fungal cell wall-degrading enzymes, lectin, and secondary metabolite biosynthetic enzymes, reflecting its mycoparasitic life style and mycotoxigenic capability. This high-quality assembly of the T. rugulosus genome will be a valuable resource to assist us in the understanding of the molecular basis of mycoparasitism and facilitate the agricultural and biotechnological applications of Talaromyces spp.

Complete chloroplast genome sequence of Stachys japonica (Labiatae)

The complete chloroplast genome of Stachys japonica was reconstructed by reference-based assembly using Illumina paired-end data. The assembled plastome is 150,599 base pairs (bp) in length, including a pair of inverted repeat regions (IRs) of 25,654 bp each, a large single-copy region (LSC) of 81,701 bp and a small single-copy region (SSC) of 17,590 bp. A total of 131 genes were predicted from the chloroplast genome, including 86 protein coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of S. japonica chloroplast genome was 38.5%. Phylogenetic analysis with several reported chloroplast genomes showed that S. japonica is closely clustered with S. sylvatica. The complete chloroplast genome of S. japonica provides new insight into Labiatae evolutionary and genomic studies.

The complete chloroplast genome of Actinidia valvata (Actinidiaceae)

The complete chloroplast (cp) genome of Actinidia valvata (A. valvata) was sequenced and assembled into a circular genome of 156,548 bp in length using Illumina paired-end data. The genome consisted of a pair of inverted repeats (IR) (23,378 bp each) separating two single-copy regions, the large single-copy region (LSC) 88,397 bp and the small single-copy region (SSC) 21,395 bp. The cp genome encoded a total of 131 genes, including 85 protein-coding genes, 38 tRNA genes, and 8 rRNA genes. The phylogenetic analysis showed that A. valvata was sister to Actinidia tetramera (A. tetramera).

Joining Illumina paired-end reads for classifying phylogenetic marker sequences

BackgroundIllumina sequencing of a marker gene is popular in metagenomic studies. However, Illumina paired-end (PE) reads sometimes cannot be merged into single reads for subsequent analysis. When mergeable PE reads are limited, one can simply use only first reads for taxonomy annotation, but that wastes information in the second reads. Presumably, including second reads should improve taxonomy annotation. However, a rigorous investigation of how best to do this and how much can be gained has not been reported.ResultsWe evaluated two methods of joining as opposed to merging PE reads into single reads for taxonomy annotation using simulated data with sequencing errors. Our rigorous evaluation involved several top classifiers (RDP classifier, SINTAX, and two alignment-based methods) and realistic benchmark datasets. For most classifiers, read joining ameliorated the impact of sequencing errors and improved the accuracy of taxonomy predictions. For alignment-based top-hit classifiers, rearranging the reference sequences is recommended to avoid improper alignments of joined reads. For word-counting classifiers, joined reads could be compared to the original reference for classification. We also applied read joining to our own real MiSeq PE data of nasal microbiota of asthmatic children. Before joining, trimming low quality bases was necessary for optimizing taxonomy annotation and sequence clustering. We then showed that read joining increased the amount of effective data for taxonomy annotation. Using these joined trimmed reads, we were able to identify two promising bacterial genera that might be associated with asthma exacerbation.ConclusionsWhen mergeable PE reads are limited, joining them into single reads for taxonomy annotation is always recommended. Reference sequences may need to be rearranged accordingly depending on the classifier. Read joining also relaxes the constraint on primer selection, and thus may unleash the full capacity of Illumina PE data for taxonomy annotation. Our work provides guidance for fully utilizing PE data of a marker gene when mergeable reads are limited.

The complete chloroplast genome sequence of Distylium macrophyllum (Hamamelidaceae)

Distylium macrophyllum H.T.Chang is a critically endangered tree species endemic to southern China. In this study, we assembled and characterized the plastome of D. macrophyllum using Illumina paired-end data. The circular genome is 159,089 bp in size, consisting of two copies of inverted repeat (IR) regions of 26,235 bp, one large single-copy (LSC) region of 87,822 bp, and one small single-copy (SSC) region of 18,797 bp. It encodes a total of 114 unique genes, including 80 protein-coding genes, 30 tRNA genes, and four rRNA genes. Phylogenetic analysis based on 13 cp genome sequences indicated that D. macrophyllum was sister to the clade of D. tsiangii and Parrotia subaequalis.

The complete chloroplast genome sequence of Rosa laevigata (Rosaceae)

The complete chloroplast genome of Rosa laevigata has been characterized by reference-based assembly using Illumina paired-end data. The complete cp genome is 156,342 bp in length, containing a large single-copy region of 85,459 bp, a small single-copy region of 18,785 bp, which are separated by a pair of inverted repeat regions of 26,049 bp, a total of 140 genes were predicted from the cp genome, including 87 protein-coding genes, 39 tRNA genes, and 8 rRNA genes . Most genes occur as a single copy, while 19 gene species are duplicated. Phylogenetic analysis reveals that R. laevigata and Rosa roxburghii f. normalis are more closely related to each other than either is to Rosa banksiae var. normalis.

The complete chloroplast genome sequence of Actinidia eriantha

The complete chloroplast (cp) genome sequence of Actinidia eriantha was sequenced and assembled using Illumina paired-end data. The cp genome from A. eriantha is 156,964 bp in length, composed of a pair of 23,892 bp inverted repeat regions (IR) separated by a large single copy region (LSC) of 88,639 bp and a small single copy region (SSC) of 20,541 bp. The cp genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNA genes, and four ribosomal RNA genes. The phylogenetic position of A. eriantha based the cp genome data was sister to the group A. rufa, A. deliciosa, and A. chinensis.

Assembly and phylogenetic analysis of the complete chloroplast genome sequence of Actinidia setosa

The complete chloroplast (cp) genome sequence of Actinidia setosa (A. setosa) was sequenced and assembled into a circular genome of 156,728 bp length using Illumina paired-end data. The cp genome composed of a pair of 24,090 bp inverted repeat (IR) regions separated by a large single copy region (LSC) of 88,256 bp and a small single copy region (SSC) of 20,292 bp. Additionally, a total of 131 genes, including 85 protein-coding genes, 38 tRNA genes and 8 rRNA genes, were identified in the A. setosa cp genome. Phylogenetic analysis showed that A. setosa was evolutionarily close to other two kiwifruits A. deliciosa and A. chinensis.

The complete chloroplast genome sequence of Rosa pricei (Rosaceae)

The complete chloroplast (cp) genome of Rosa pricei Hayata has been characterized by reference-based assembly using Illumina paired-end data. The complete cp genome is 156,599 base pairs (bp) in length, containing a large single-copy region (LSC) of 85,732 bp, a small single-copy region (SSC) of 18,749 bp, which are separated by a pair of inverted repeat regions (IRs) of 26,059 bp, a total of 139 genes were predicted from the chloroplast genome, including 87 protein-coding genes, 39 tRNA genes, and eight rRNA genes (four rRNA species). Most genes occur as a single copy while 19 gene species are duplicated. Phylogenetic analysis revealed that R. pricei was resolved as sister to R. multiflora, R. lucieae, and R. maximowicziana.

The complete chloroplast genome sequence of Rosa banksiae var. normalis (Rosaceae)

The complete chloroplast genome of Rosa banksiae var. normalis was reconstructed by reference-based assembly using Illumina paired-end data. The assembled plastome is 156,575 base pairs (bp) in length, including a pair of inverted repeat regions (IRs) of 26,008 bp each, a large single copy region (LSC) of 85,792 bp, and a small single copy region (SSC) of 18,767 bp. A total of 129 genes were predicted from the chloroplast genome, including 84 protein coding genes, 37 tRNA genes and 8 rRNA genes. The overall GC content of Rosa banksiae var. normalis chloroplast genome was 37.22%. Phylogenetic analysis with several reported chloroplast genomes showed that Rosa banksiae var. normalis is closely clustered with Rosa odorata var. gigantea, Rosa multiflora, Rosa chinensis var. spontanea, and Rosa roxburghii. The complete chloroplast genome of Rosa banksiae var. normalis provides new insight into Rosaceae evolutionary and genomic studies.

The complete chloroplast genome sequence of Actinidia Callosa Var. Henryi

The complete chloroplast (cp) genome sequence of Actinidia callosa var. henryi was assembled and characterize by Illumina paired-end data in this study. The assembled plastome was 156,826 bp in length, containing a large single copy region (LSC) of 88,604 bp and a small single copy region (SSC) of 22,510 bp, which was separated by a pair of 23,866 bp inverted repeat regions (IR). The genome possessed 127 genes, including 82 protein-coding genes, 37 tRNA genes, 8 ribosomal RNA genes. The phylogenetic position based on the chloroplast genome showed that Actinidia callosa var. henryi was sister to the group A. eriantha, A. deliciosa, and A. chinensis.

The complete chloroplast genome sequence of Actinidia zhejiangensis

The complete chloroplast (cp) genome sequence of Actinidia zhejiangensis was assembled and characterized by Illumina paired-end data in this study. The complete chloroplast genome of Actinidia zhejiangensis is 156,717 bp in length, containing a large single copy region (LSC) of 86,483 bp and a small single copy region (SSC) of 22,574 bp, which was separated by a pair of 23,840 bp inverted repeat regions (IR). A total of 128 genes are detected, including 81 protein-coding genes, 39 tRNA genes, 8 ribosomal RNA genes. The phylogenetic position based on the chloroplast genome showed that Actinidia zhejiangensis was sister to the group A. deliciosa and A. chinensis.

The complete chloroplast genome sequence of Olmediella betschleriana and its phylogenetic analysis

The complete chloroplast genome of Olmediella betschleriana was reconstructed by reference-based assembly using Illumina paired-end data. The assembled plastome is 158,171 base pairs (bp) in length, including a pair of inverted repeat regions (IRs) of 27,900 bp each, a large single-copy region (LSC) of 85,783 bp and a small single-copy region (SSC) of 16,588 bp. A total of 119 genes were predicted from the chloroplast genome, including 83 protein-coding genes, 36 tRNA genes, and 8 rRNA genes. The overall GC content of O. betschleriana chloroplast genome was 36.71%. The phylogenetic analysis with 15 other species showed that O. betschleriana was closely clustered with Idesia polycarpa. The complete chloroplast genome of O. betschleriana provides new insight into Salicaceae evolutionary and genomic studies.